BCR-ABL1 Mutation Analysis for Tyrosine Kinase Inhibitor Resistance

Last Literature Review: August 2020 Last Update:
  • Order only for patients with an established diagnosis of a BCR-ABL1-positive leukemia
  • Use to determine if a mutation is present that would interfere with response to TKI therapy in Ph+ ALL or CML
    • Detects all common mutations, including T315I
    • Higher sensitivity than traditional Sanger sequencing techniques
    • Offers coverage of SH2, SH3, and kinase domain

BCR-ABL1 mutations may cause resistance to tyrosine kinase inhibitor (TKI) therapy in patients with either chronic myelogenous leukemia (CML) or Philadelphia chromosome positive (Ph+) acute lymphoblastic leukemia (ALL). Testing should be performed for patients with an established diagnosis of a BCR-ABL1-positive leukemia to guide treatment decisions.

Disease Overview

Treatment Issues

Chronic Myelogenous Leukemia

  • CML is characterized by BCR-ABL1 translocations
  • Initial treatment protocol is TKI therapy
    • Imatinib (Gleevec) inhibits tyrosine kinase activity caused by the BCR-ABL1 gene fusion
    • Dasatinib (Sprycel) is a dual specific SRC/ABL inhibitor
    • Nilotinib (Tasigna) is an imatinib derivative with 30-fold potency compared to imatinib
  • Resistance to TKI therapy may result from acquired point mutations within the ABL kinase domain, BCR-ABL1 amplification, low bioavailability, and/or quiescent CML stem cells
    • Resistance may be overcome with dose adjustments or a change in therapy
    • Newer drugs may be useful when resistance develops, including bosutinib (Bosulif) and ponatinib (Iclusig)
  • Use of massively parallel sequencing (next generation sequencing) improves the ability to detect low-level clones across larger sections of the gene

Acute Lymphoblastic Leukemia

BCR-ABL1 mutations are present in a subset of ALL patients and are more common in adults than children. Detection of mutations in BCR-ABL1 is important in helping to determine potential response to TKI therapy.


Gene Fusion



  • >130 mutations
  • Four regions tested: adenosine triphosphate binding-loop (P-loop), drug-binding sites, catalytic domain, and activation loop

Test Interpretation

Analytical Sensitivity

  • Variant class: single nucleotide variant (SNV)
  • Number of variants tested: 396
  • Positive percent agreement (PPA): 96.3%
  • PPA, 95% tolerance at 95% reliability: 94.3-98.0%


DetectedMutation detected in the SH2, SH3, or kinase domain (ABL1 amino acid residues 46-542)
Not amplifiedMultiple attempts to amplify the BCR-ABL1 translocation were unsuccessful by PCR
Not detectedNo mutation detected
PCR, polymerase chain reaction


  • A negative result does not exclude mutations below the level of detection or outside the sequenced region
  • Sensitivity of this assay may be limited, and sequencing may not be possible in patient samples containing low tumor burden (ie, low levels of BCR-ABL1 fusion transcript by international scale % or normalized copy number)
  • Not intended to be used for detection or quantification of BCR-ABL1 fusion transcripts